@article {545, title = {Functional-State Dependence of Picosecond Protein Dynamics}, journal = {J. Phys. Chem. B}, volume = {125}, year = {2021}, pages = {11134-11140}, chapter = {11134}, abstract = {

We examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E1 \~{} 0.1 kJ/mol and E2 \~{} 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent{\textendash}protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.

}, doi = {10.1021/acs.jpcb.1c05018}, author = {George, D. K. and Chen, J. Y. and He, Yunfen and Knab, J. R. and Markelz, A. G.} } @article {291, title = {Functional State Dependence of Picosecond Protein Dynamics}, journal = {arXiv:1105.4425}, year = {2012}, url = {http://arxiv.org/0054394}, author = {Chen, J. Y. and George, D. K. and He, Y. and Knab, J. R. and Markelz, A.G.} } @article {292, title = {Why is THz Sensitive to Protein Functional States? Oxidation State of Cytochrome C}, journal = {Terahertz Science and Technology}, volume = {3}, year = {2010}, chapter = {149-162}, abstract = {

We investigate the presence of structural collective motions on a picosecond time scale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time-domain spectroscopy and molecular dynamics simulations. Structural collective mode frequencies have been calculated to lie in this frequency range, and the density of states can be considered a measure of flexibility. A dramatic increase in the THz response occurs with oxidation, with the largest increase for lowest hydrations and highest frequencies. For both oxidation states the measured THz response rapidly increases with hydration saturating above ~25\% (g H2O/g protein), in contrast to the rapid turn-on in dynamics observed at this hydration level for other proteins. Quasi-harmonic collective vibrational modes and dipole-dipole correlation functions are calculated from the molecular dynamics trajectories. The collective mode density of states alone reproduces the measured hydration dependence providing strong evidence of the existence of these collective motions. The large oxidation dependence is reproduced only by the dipole-dipole correlation function, indicating the contrast arises from diffusive motions consistent with structural changes occurring in the vicinity of a buried internal water molecule.

}, doi = {10.11906/TST.149-162.2010.12.15}, url = {http://www.tstnetwork.org/10.11906/TST.149-162.2010.12.15/}, author = {He,Y. and Chen, J.-Y. and Knab, J. R. and Zheng, W. and Markelz, A.G.} } @inbook {303, title = {Development of Tagless Biosensors for Detecting the Presence of Pathogens}, booktitle = {Terahertz Frequency Detection and Identification of Materials and Objects}, volume = {ed X.-C. Zhang, R. E. Miles, H. Eisele and A. Krotkus}, year = {2007}, pages = {123-134}, publisher = {Springer}, organization = {Springer}, chapter = {9}, address = {Dordrecht, The Netherlands}, author = {Markelz, A. G. and Chen, J.-Y. and Knab, J. R. and He, Y. and Ye, S.} } @article {223, title = {Terahertz dielectric assay of solution phase protein binding}, journal = {Applied Physics Letters}, volume = {90}, number = {24}, year = {2007}, note = {ISI Document Delivery No.: 179QR
Times Cited: 51
Cited Reference Count: 9
Cited References:
Balog E, 2004, PHYS REV LETT, V93, DOI 10.1103/PhysRevLett.93.028103
Brucherseifer M, 2000, APPL PHYS LETT, V77, P4049, DOI 10.1063/1.1332415
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Fear G, 2007, PHARMACOL THERAPEUT, V113, P354, DOI 10.1016/j.pharmthera.2006.09.001
Heugen U, 2006, P NATL ACAD SCI USA, V103, P12301, DOI 10.1073/pnas.0604897103
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Menikh A, 2004, BIOSENS BIOELECTRON, V20, P658, DOI 10.1016/j.bios.2004.03.006
Xu J, 2006, PROTEIN SCI, V15, P1175, DOI 10.1110/ps.062073506
Chen, Jing-Yin Knab, J. R. Ye, Shuji He, Yunfen Markelz, A. G.
Ye, Shuji/B-4479-2010
Markelz, Andrea/0000-0003-0443-4319
53
1
42
Amer inst physics
Melville
1077-3118}, month = {Jun}, pages = {3}, type = {Article}, abstract = {

The authors demonstrate a method for rapid determination of protein-ligand binding on solution phase samples using terahertz dielectric spectroscopy. Measurements were performed using terahertz time domain spectroscopy on aqueous solutions below the liquid-solid transition for water. Small ligand binding sensitivity was demonstrated using triacetylglucosamine and hen egg white lysozyme with a decrease in dielectric response with binding. The magnitude of the change increases with frequency. (c) 2007 American Institute of Physics.

}, keywords = {dynamics, lysozyme, Physics, spectroscopy, water}, isbn = {0003-6951}, doi = {10.1063/1.2748852}, author = {Chen, J. Y. and Knab, J. R. and Ye, S. J. and He, Y. F. and Markelz, A. G.} } @article {229, title = {Terahertz transmission characteristics of high-mobility GaAs and InAs two-dimensional-electron-gas systems}, journal = {Applied Physics Letters}, volume = {89}, number = {13}, year = {2006}, note = {ISI Document Delivery No.: 089JE
Times Cited: 18
Cited Reference Count: 16
Cited References:
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Kabir, N. A. Yoon, Y. Knab, J. R. Chen, J. -Y. Markelz, A. G. Reno, J. L. Sadofyev, Y. Johnson, S. Zhang, Y. -H. Bird, J. P.
Bird, Jonathan P/G-4068-2010
Bird, Jonathan P/0000-0002-6966-9007; Markelz, Andrea/0000-0003-0443-4319
18

15
Amer inst physics
Melville}, month = {Sep}, pages = {3}, type = {Article}, abstract = {

Frequency-dependent complex conductivity of high-mobility GaAs and InAs two-dimensional-electron-gas (2DEG) systems is studied by terahertz time domain spectroscopy. Determining the momentum relaxation time from a Drude model, the authors find a lower value than that from dc measurements, particularly at high frequencies/low temperatures. These deviations are consistent with the ratio tau(t)/tau(q,) where tau(q) is the full scattering time. This suggests that small-angle scattering leads to weaker heating of 2DEGs at low temperatures than expected from dc mobilit9y. (c) 2006 American Institute of Physics.

}, keywords = {field-effect transistors, photoconductivity, Physics, plasma-waves, radiation, resonant detection, subterahertz}, isbn = {0003-6951}, doi = {10.1063/1.2357605}, author = {Kabir, N. A. and Yoon, Y. and Knab, J. R. and Chen, J. Y. and Markelz, A. G. and Reno, J. L. and Sadofyev, Y. and Johnson, S. and Zhang, Y. H. and Bird, J. P.} } @proceedings {309, title = {Using terahertz spectroscopy as a protein binding assay}, volume = {Proc SPIE 6080,}, year = {2006}, month = {02/2006}, pages = {35-42}, address = { San Jose, California, United States}, abstract = {

The vibrational modes corresponding to protein tertiary structural motion lay in the far infrared or terahertz frequency range. These collective large scale motions depend on global structure and thus will necessarily be perturbed by ligand binding events. We discuss the use of terahertz dielectric spectroscopy to measure these vibrational modes and the sensitivity of the technique to changes in protein conformation, oxidation state and environment. A challenge of applying this sensitivity as a spectroscopic assay for ligand binding is the sensitivity of the technique to both bulk water and water bound to the protein. This sensitivity can entirely obscure the signal from the protein or protein-ligand complex itself, thus necessitating sophisticated sample preparation making the technique impractical for industrial applications. We discuss methods to overcome this background and demonstrate how terahertz spectroscopy can be used to quickly assay protein binding for proteomics and pharmaceutical research.

}, doi = {10.1117/12.664098}, author = {Chen, J.-Y. and Knab, J. R. and Ye, S. and He, Y. and Markelz, A. G.} } @article {263, title = {Large oxidation dependence observed in terahertz dielectric response for cytochrome c}, journal = {Physical Review E}, volume = {72}, number = {4}, year = {2005}, note = {ISI Document Delivery No.: 979GO
Times Cited: 51
Cited Reference Count: 29
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Chen, JY Knab, JR Cerne, J Markelz, AG
Markelz, Andrea/0000-0003-0443-4319
52

22
Amer physical soc
College pk
1550-2376
1}, month = {Oct}, pages = {4}, type = {Article}, abstract = {

Far infrared dielectric response is used to characterize the collective mode density of states for cytochrome c as a function of oxidation state and hydration using terahertz time domain spectroscopy. A strong absorbance and refractive index increase was observed with the oxidation. A simple phenomenological fitting using a continuous distribution of oscillators reproduces the frequency dependence of the complex dielectric response as well as demonstrates quantitative agreement with a uniform increase in either mode density or polarizability with oxidation in the 5-80 cm(-1) frequency range. Hydration dependence measurements find that a difference in the equilibrium water content for ferri and ferro cytochrome c is not sufficient to account for the large change in terahertz response. The large dielectric increase at terahertz frequencies with oxidation suggests either a significant global softening of the potential and/or a significant increase in polarizability with oxidation.

}, keywords = {absorption, binding, conformation, dna, dynamics, heart ferricytochrome-c, modes, Physics, protein flexibility, spectroscopy, state}, isbn = {1539-3755}, doi = {10.1103/PhysRevE.72.040901}, author = {Chen, J. Y. and Knab, J. R. and Cerne, J. and Markelz, A. G.} } @article {234, title = {Protein dynamics studies using terahertz dielectric response}, journal = {Abstracts of Papers of the American Chemical Society}, volume = {230}, year = {2005}, note = {ISI Document Delivery No.: 032TJ
Times Cited: 0
Cited Reference Count: 0
Markelz, A. G. Knab, J. R. Chen, J. -Y.
230th National Meeting of the American-Chemical-Society
Aug 28-sep 01, 2005
Washington, DC
Amer Chem Soc

2
Amer chemical soc
Washington}, month = {Aug}, pages = {U347-U348}, type = {Meeting Abstract}, keywords = {Chemistry}, isbn = {0065-7727}, doi = {10.1016/j.cplett.2007.05.080}, author = {Markelz, A. G. and Knab, J. R. and Chen, J. Y.} } @proceedings {311, title = {Measuring Protein Flexibility with Terahertz Spectroscopy: Basic Research and Applications}, year = {2004}, month = {06/2004}, address = {San Diego, CA}, doi = {10.1109/LEOSST.2004.1338649}, author = {Markelz, A. G. and Chen, J.-Y. and Knab, J. R. and Maeder, M.} } @proceedings {310, title = {Terahertz measurements of the Photoactive Protein Bacteriorhodopsin mutant D96N: M and P states}, volume = {826}, year = {2004}, pages = {pages261{\textendash}267}, address = {Warrendale, PA}, abstract = {

We use terahertz (THz) spectroscopy as a biomaterials characterization tool. Previously we have shown a strong contrast between the THz dielectric response for wild type (WT) and D96N mutant of bacteriorhodopsin. In those studies we observed a large increase in the THz absorbance of WT with excitation to thermally captured photo-intermediates whereas no such increase in absorbance was observed for the mutant D96N. These results suggest that the THz response is sensitive to structural changes and relative flexibility of biomolecules. However the photo-intermediate populations of the WT and D96N samples were not equivalent in those measurements. While the WT samples had relaxed (bR), M and P state intermediates present, the D96N samples had only bR and M states. Here we present terahertz absorbance measurements of D96N as a function of M and P state populations at room temperature. The THz response is constant for intermediate states populations up to 23\% M state and up to 30\% P state. These results verify that there is a fundamental difference in the conformational dynamics as measured by THz dielectric response for a single residue mutation.

}, doi = {10.1557/PROC-826-V2.6}, author = {Chen, C.-Y. and Knab, J. R. and Cerne, J. and Hillebrecht, J. R. and Birge, R. R. and Markelz, A. G.} } @proceedings {312, title = {Thz Dielectric Response As A Function Of Protein Hydration: Intramolecular Coupling Contribution}, year = {2004}, month = {10/2004}, address = {Philadelphia, PA}, author = {Markelz, A. G. and Chen, J.-Y. and Knab, J. R. and Maeder, M.} }